Re: [Jmol-users] New menu item "Identity"?

yes, it just does
set picking ident
which is the default mode for picking.
Eric Martz wrote:
>At 7/24/07, Bob Hanson wrote:
>
>
>>translations needed for the new "Identity" menu item.
>>
>>
>
>The only "Identity" item I find on the menu of 11.3.6 is under "Set
>Picking". Is that the new item to which you refer?
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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Dear Bob,
Herb Bernstein's recent message to molvis-list and pdb-l about RasMol
being revised to support PDB format version 3 alerted me to a
potential problem that I had not been aware of.
As part of the PDB's remediation project (
http://remediation.wwpdb.org/ ), they made changes to the PDB format,
now called version 3. Notably, DNA nucleotides are named DA, DT, DC,
DG, DI while RNA remain A, U, C, G, I.
Apparently within a matter of weeks, all PDB files from the wwPDB
will be in remediated format, including of course all new future entries.
So far I have not managet personally to test the consequences of the
remediated PDB format e.g. for FirstGlance in Jmol. However, at least
the change in DNA naming seems likely to me to require changes within
Jmol itself.
So this is a heads up, in case this has not already been dealt with.
Regards, -Eric

On 18 Jul 2007 at 15:22, Eric Martz wrote:
> As part of the PDB's remediation project (
> http://remediation.wwpdb.org/ ), they made changes to the PDB format,
> now called version 3. Notably, DNA nucleotides are named DA, DT, DC,
> DG, DI while RNA remain A, U, C, G, I.
Hello. I was also wondering what the "new V3" format would mean in practice, but had not
read through any details.
wwPDB documentation at
http://remediation.wwpdb.org/software.html
says literally:
"...software tools that are compatible with the nomenclature that is used in PDB Version 3.0
(remediated) and PDB Version 3.1 (data released after August 1, 2007)."
and the list includes "JMol V11.2.4" !!!
> So far I have not managet personally to test the consequences of the
> remediated PDB format e.g. for FirstGlance in Jmol. However, at least
> the change in DNA naming seems likely to me to require changes within
> Jmol itself.
I have quickly tested a couple of files, 1asy.pdb (protein + RNA) and 1bna.pdb (DNA), in
remediated format (gzipped), and they give no trouble in 11.2.4
For example, "select nucleic", "select dna" , "select rna" work in both.
In 1bna, "select a" works, but "select [A]" selects nothing since the residues are named DA;
"select [DA]" does work, same as "select a"
"select t" does not work **this needs fixing**. "select dt" works ok
"select backbone", "select sidechain", "select bases", "select purine", "select pyrimidine",
"select cg" all work OK
"select at" selects adenosines only **this needs fixing** probbaly because select t is not
working (see above)
"select au" does not work
"select u" selects thymidines in DNA !!
So, for the most part, I see that Jmol is taking care of this particular change. We need to
make sure, though, that there aren't any other relevant changes in the format.

Angel, could you please double check now and see if Jmol 11.2.5 works as
you expect in this regard?
translations needed for the new "Identity" menu item.
Bob
Angel Herraez wrote:
>On 18 Jul 2007 at 15:22, Eric Martz wrote:
>
>
>>As part of the PDB's remediation project (
>>http://remediation.wwpdb.org/ ), they made changes to the PDB format,
>>now called version 3. Notably, DNA nucleotides are named DA, DT, DC,
>>DG, DI while RNA remain A, U, C, G, I.
>>
>>
>
>Hello. I was also wondering what the "new V3" format would mean in practice, but had not
>read through any details.
>
>wwPDB documentation at
>http://remediation.wwpdb.org/software.html
>says literally:
>"...software tools that are compatible with the nomenclature that is used in PDB Version 3.0
>(remediated) and PDB Version 3.1 (data released after August 1, 2007)."
>and the list includes "JMol V11.2.4" !!!
>
>
>
>>So far I have not managet personally to test the consequences of the
>>remediated PDB format e.g. for FirstGlance in Jmol. However, at least
>>the change in DNA naming seems likely to me to require changes within
>>Jmol itself.
>>
>>
>
>I have quickly tested a couple of files, 1asy.pdb (protein + RNA) and 1bna.pdb (DNA), in
>remediated format (gzipped), and they give no trouble in 11.2.4
>
>For example, "select nucleic", "select dna" , "select rna" work in both.
>
>In 1bna, "select a" works, but "select [A]" selects nothing since the residues are named DA;
>"select [DA]" does work, same as "select a"
>
>"select t" does not work **this needs fixing**. "select dt" works ok
>
>"select backbone", "select sidechain", "select bases", "select purine", "select pyrimidine",
>"select cg" all work OK
>
>"select at" selects adenosines only **this needs fixing** probbaly because select t is not
>working (see above)
>
>"select au" does not work
>
>"select u" selects thymidines in DNA !!
>
>
>
>So, for the most part, I see that Jmol is taking care of this particular change. We need to
>make sure, though, that there aren't any other relevant changes in the format.
>
>
>
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>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

At 7/24/07, Bob Hanson wrote:
>translations needed for the new "Identity" menu item.
The only "Identity" item I find on the menu of 11.3.6 is under "Set
Picking". Is that the new item to which you refer?

yes, it just does
set picking ident
which is the default mode for picking.
Eric Martz wrote:
>At 7/24/07, Bob Hanson wrote:
>
>
>>translations needed for the new "Identity" menu item.
>>
>>
>
>The only "Identity" item I find on the menu of 11.3.6 is under "Set
>Picking". Is that the new item to which you refer?
>
>
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>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

Dear Bob,
I have now done some tests on nucleic acids for the old vs. new PDB
formats. The old format, version 2.3, has been in effect since 1998.
The new "remediated" version goes into effect August 1, 2007.
Differences are summarized in
http://www.wwpdb.org/documentation/format3.1-20070719.pdf
In my tests, unless otherwise noted, I used Jmol 11.3.6.
-----------------------
1. BUG: "select dna" select DNA or RNA:
"select dna" seems to me to have a bug: it selects rna as well as
dna. A good test PDB file is 104D (PDB new format 3), which has both
(510 DNA atoms and 256 RNA Atoms). So, in 104D, "select dna" selects
766 atoms, surely not the desired behavior.
This bug was NOT PRESENT in Jmol 10.2.0 (still in use in the main
public FirstGlance in Jmol version 1.0), but WAS PRESENT in Jmol
11.1.27 as well as in Jmol 11.3.6.
----------------------
2. OK: "select t" selects thymidine in 104D (128 atoms).
"select [t]" selects 0 atoms, which seems correct since thymidine now
has the group name DT.
"select dt" and "select [dt]" both work (128 atoms).
----------------------
3. ??: Things get more problematic with "select a,c,g" because these
select both DNA and RNA. Now that DNA residues are named DA, DC, and
DG, is this the desired behavior?
Tests with 104D:
"select g" gets 270 atoms, including both DNA and RNA guanosines.
"select [g]" gets only 136 atoms, the RNA G atoms, confirmed with
"select rna and [g]". This is correct because the DNA G atoms are named DG.
"select [dg]" or "select dg" gets 134 atoms (DNA G).
"select [dg],[g]" gets the same as "select g", 270 atoms (DNA G + RNA G).
However, since "select dna" gets all RNA, "select dna and [g]" gets
the 136 RNA G atoms.
----------------------
4. BUGS?
Using 1EVV (new PDB format) in Jmol 11.3.6, there are some things I
don't understand.
"select 2mg" selects [C2]:A and [HOH]2, but not the one residue named 2MG.
"select [2mg]" correctly selects the latter, [2MG]10:A.
"select 5mu" behaves similarly.
"select [5mu] and 5mu" gets 0 atoms, consistent with the above
(buggy?) behavior.
However, reversing the order,
"select 5mu and [5mu]" generates an error, as does also
"select 5mu and rna"
script compiler ERROR: end of expression expected
--------------------------
--------------------------
I think I've found some additional anomalies but I need to do more
testing to be sure. More on those later, if I can confirm them.
-Eric

Thank you very much for doing these tests, Eric.
Eric Martz wrote:
>Dear Bob,
>
>I have now done some tests on nucleic acids for the old vs. new PDB
>formats. The old format, version 2.3, has been in effect since 1998.
>The new "remediated" version goes into effect August 1, 2007.
>Differences are summarized in
>http://www.wwpdb.org/documentation/format3.1-20070719.pdf
>
>In my tests, unless otherwise noted, I used Jmol 11.3.6.
>
>-----------------------
>1. BUG: "select dna" select DNA or RNA:
>
>"select dna" seems to me to have a bug: it selects rna as well as
>dna. A good test PDB file is 104D (PDB new format 3), which has both
>(510 DNA atoms and 256 RNA Atoms). So, in 104D, "select dna" selects
>766 atoms, surely not the desired behavior.
>
>This bug was NOT PRESENT in Jmol 10.2.0 (still in use in the main
>public FirstGlance in Jmol version 1.0), but WAS PRESENT in Jmol
>11.1.27 as well as in Jmol 11.3.6.
>
>
>
This should be fixed in 11.3.7, 11.2.7. It was a bug introduced in
association with a fix I created last November that has the comment:
"Fixes phosphorus-only dna/rna rendering/selecting problem."
>----------------------
>2. OK: "select t" selects thymidine in 104D (128 atoms).
>
>"select [t]" selects 0 atoms, which seems correct since thymidine now
>has the group name DT.
>
>"select dt" and "select [dt]" both work (128 atoms).
>
>
>
so we will accept this a correct behavior
>----------------------
>3. ??: Things get more problematic with "select a,c,g" because these
>select both DNA and RNA. Now that DNA residues are named DA, DC, and
>DG, is this the desired behavior?
>
>
>
yes.
>Tests with 104D:
>
>"select g" gets 270 atoms, including both DNA and RNA guanosines.
>
>"select [g]" gets only 136 atoms, the RNA G atoms, confirmed with
>"select rna and [g]". This is correct because the DNA G atoms are named DG.
>
>"select [dg]" or "select dg" gets 134 atoms (DNA G).
>"select [dg],[g]" gets the same as "select g", 270 atoms (DNA G + RNA G).
>
>However, since "select dna" gets all RNA, "select dna and [g]" gets
>the 136 RNA G atoms.
>
>
>
fix should now give:
select dna and [g]
0 atoms selected
>----------------------
>4. BUGS?
>Using 1EVV (new PDB format) in Jmol 11.3.6, there are some things I
>don't understand.
>
>"select 2mg" selects [C2]:A and [HOH]2, but not the one residue named 2MG.
>"select [2mg]" correctly selects the latter, [2MG]10:A.
>
>
>
The compiler is reading "select 2mg" as
"select 2 mg" and then just using "select 2"
It's a bug. I will look into it, but not for 11.3.7/11.2.7
>"select 5mu" behaves similarly.
>
>"select [5mu] and 5mu" gets 0 atoms, consistent with the above
>(buggy?) behavior.
>
>However, reversing the order,
>"select 5mu and [5mu]" generates an error, as does also
>"select 5mu and rna"
>script compiler ERROR: end of expression expected
>
>--------------------------
>--------------------------
>
>I think I've found some additional anomalies but I need to do more
>testing to be sure. More on those later, if I can confirm them.
>
>-Eric
>
>
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>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

Have we a facility to centre (single) labels on a number of atoms, or the
space between them?
I am thinking of labelling R-groups on amino-acids, or labelling cavities
within molecules.
Richard Steane
Near Guildford, Surrey, UK
Website http://www.BioTopics.co.uk dedicated to teaching and learning
Biology